Average distribution in gastric cancer patient biopsies

**Figure 3.** *Cont*.

**Figure 3.** Comparison of the bacterial reads from microbiome analysis of unwashed and washed biopsies from (**a**) dyspepsia patients and (**b**) gastric cancer patients (percentages are listed in Table 4). Comparison of (**c**) the alpha-diversity shown by a Shannon Index, *p* = 0.22581 and (**d**) the beta-diversity between the two groups shown by PCoA plot, *p* = 0.801199, in unwashed biopsies (red) and washed biopsies (blue).

#### *3.2. Comparison of Biopsies from Gastric Cancer Patients and Dyspepsia Patients*

#### 3.2.1. Cultured Bacteria were Dominated by *Streptococcus* spp.

The biopsies from dyspepsia patients and gastric cancer patients were dominated by similar cultured bacteria (Figure 4). Species of *Lactobacillus* were cultured from several cancer patient biopsies but only from one dyspepsia patient biopsy (Table 2). The distribution of cultured bacteria in biopsies from gastric cancer patients and dyspepsia patients showed an increase in the relative abundance of *Streptococcus* and a decrease in *Actinomyces* spp. (Table 3, Figure 4).

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5HODWLYHGLVWULEXWLRQRIFXOWXUHG*non-Helicobacter*  EDFWHULD

**Figure 4.** The relative distribution of non-*Helicobacter* bacteria cultured from the unwashed biopsies showed that *Streptococcus* spp. were predominant in both dyspepsia patients and gastric cancer patients. The percentages can be found in Table 3. "Others" include *Bacillus* spp., *Corynebacterium* spp., *Enterobacter* spp., *Enterococcus* spp., *Haemophilus* spp, *Micrococcus* spp., *Neisseria* spp., and *Stenotrophomonas* spp.

3.2.2. Microbiome Analysis Revealed Similar Distributions of Bacteria in Dyspepsia Patients and Gastric Cancer Patients

The average relative abundance of *H. pylori* was not significantly different in untreated biopsies untreated dyspepsia patients and gastric cancer patients (Figure 5a). For most bacterial groups, no significant difference was observed in the distribution of bacteria between dyspepsia patient and gastric cancer patient biopsies. However, a significant increase in the presence of *Prevotella* spp. was observed in dyspepsia patients (*p* = 0.0109) and of "other bacteria" in gastric cancer patients (*p* = 0.0349). This increase in other bacteria may be explained by the dominance of *Enterococcus* spp. in one biopsy pair, where more than 95% of the bacterial reads were identified as this. If this biopsy pair was removed from the data, the difference in "other bacteria" between the patient groups was not significant. The bacterial diversity in biopsies from dyspepsia patients and gastric cancer patients showed no significant differences within the groups (Figure 5b) or between the distribution of species in the groups (Figure 5c).
